mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 209 | C→T | T7I (ACC→ATC) | thrL → | thr operon leader peptide |
| RA | 173,011 | A→G | Y517C (TAC→TGC) | fhuB → | iron(3+)‑hydroxamate import ABC transporter permease |
| RA | 222,672 | A→G | intergenic (‑27/‑161) | metN ← / → gmhB | DL‑methionine transporter subunit/D,D‑heptose 1,7‑bisphosphate phosphatase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 300,196 | A→G | F247L (TTC→CTC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | ECP production outer membrane protein |
| RA | 323,369 | G→A | V344V (GTG→GTA) | ykgF → | ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component |
| RA | 661,068 | A→G | L104P (CTT→CCT) | ybeF ← | LysR family putative transcriptional regulator |
| RA | 824,554 | (A)5→6 | intergenic (‑57/‑76) | ybhP ← / → ybhQ | endo/exonuclease/phosphatase family protein/inner membrane protein |
| RA | 851,102 | T→C | K499R (AAA→AGA) | opgE ← | OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 890,497 | C→T | *86* (TGA→TAA) | grxA ← | glutaredoxin 1, redox coenzyme for ribonucleotide reductase (RNR1a) |
| RA | 959,180 | A→G | E123E (GAA→GAG) | aroA → | 5‑enolpyruvylshikimate‑3‑phosphate synthetase |
| RA | 1,055,493 | G→A | A229V (GCA→GTA) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,217,830 | T→C | V168A (GTA→GCA) | ycgG → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,685,757 | G→A | H278Y (CAC→TAC) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,881,353 | C→T | A153T (GCC→ACC) | dmlR ← | transcriptional activator of dmlA |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,230,157 | G→A | L77L (CTG→TTG) | dusC ← | tRNA‑dihydrouridine synthase C |
| RA | 2,261,060 | T→C | A117A (GCA→GCG) | fruA ← | fused fructose‑specific PTS enzymes: IIBcomponent/IIC components |
| RA | 2,482,295 | G→A | P349S (CCT→TCT) | emrK ← | multidrug resistance efflux pump membrane fusion protein |
| RA | 2,502,577 | G→A | P637S (CCG→TCG) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,687,071 | T→C | *113* (TAA→TGA) | glnB ← | regulatory protein P‑II for glutamine synthetase |
| RA | 2,756,933 | G→A | E259K (GAG→AAG) | intA → | CP4‑57 prophage; integrase |
| RA | 2,757,236 | G→A | A360T (GCG→ACG) | intA → | CP4‑57 prophage; integrase |
| RA | 2,763,681 | T→C | T491T (ACA→ACG) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,794,154 | G→A | intergenic (+139/‑99) | gabT → / → gabP | 4‑aminobutyrate aminotransferase, PLP‑dependent/gamma‑aminobutyrate transporter |
| RA | 2,810,153 | Δ1 bp | coding (537/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,854,172 | G→A | V307M (GTG→ATG) | hypE → | carbamoyl dehydratase, hydrogenases 1,2,3 maturation protein |
| RA | 2,918,955 | T→C | E144G (GAA→GGA) | gudD ← | D‑glucarate dehydratase 1 |
| RA | 3,411,876 | T→C | V75A (GTT→GCT) | yhdJ → | DNA adenine methyltransferase, SAM‑dependent |
| RA | 3,453,126 | A→G | F49L (TTC→CTC) | rpsJ ← | 30S ribosomal subunit protein S10 |
| RA | 3,462,909 | C→T | A189V (GCC→GTC) | gspJ → | putative general secretory pathway component, cryptic |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,609,639 | G→A | L141L (CTG→CTA) | yhhQ → | DUF165 family inner membrane protein |
| RA | 3,619,269 | A→G | V26V (GTA→GTG) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,619,272 | T→C | R27R (CGT→CGC) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,622,299 | G→A | T1036T (ACG→ACA) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,622,314 | G→A | R1041R (AGG→AGA) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,622,316 | G→C | S1042T (AGC→ACC) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,628,900 | T→C | E213E (GAA→GAG) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| RA | 3,815,810 | Δ1 bp | intergenic (‑42/+24) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,951,559 | +A | pseudogene (18/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,168,472 | G→A | intergenic (+25/‑169) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA of rrnB operon |
| RA | 4,168,475 | 2 bp→TG | intergenic (+28/‑165) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA of rrnB operon |
| RA | 4,168,571 | G→A | intergenic (+124/‑70) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA of rrnB operon |
| RA | 4,168,618 | A→T | intergenic (+171/‑23) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA of rrnB operon |
| RA | 4,187,507 | A→C | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,239,245 | (G)5→6 | coding (1612/2097 nt) | yjbH → | DUF940 family extracellular polysaccharide protein |
| RA | 4,288,058 | A→G | T99A (ACC→GCC) | nrfA → | nitrite reductase, formate‑dependent, cytochrome |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| MC JC | 4,397,624 | (GCTGGC)3→2 | coding (213‑218/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| RA | 4,428,993 | A→G | Q20R (CAG→CGG) | fklB → | FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423790–3424554 | 3424554 | 1–765 | 70 [69] | [69] 70 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 17 (0.130) | 97 (0.800) | 81/566 | 0.5 | 88.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 10 (0.080) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 17 (0.130) | 119 (0.980) | 97/566 | 0.1 | 90.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 10 (0.080) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||